iDNA vaccines and methods for using the same

ABSTRACT

Described herein are iDNA vectors and vaccines and methods for using the same. The iDNA generates live attenuated vaccines in eukaryotic cells in vitro or in vivo for pathogenic RNA viruses, particularly yellow fever virus and Venezuelan equine encephalitis virus. When iDNA is injected into the vaccine recipient, RNA of live attenuated virus is generated by in vivo transcription in the recipient&#39;s tissues. This initiates production of progeny attenuated viruses in the tissues of the vaccine recipient, as well as elicitation of an effective immune response protecting against wild-type, non-attenuated virus.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 14/168,788, filed Jan. 30, 2014, now allowed, which claims priority to U.S. application Ser. No. 13/054,372, filed Jun. 15, 2011, now U.S. Pat. No. 8,691,563, issued Apr. 8, 2014, which is a national stage filing under 35 U.S.C. § 371 of International Application No. PCT/US 2009/004133, filed on Jul. 17, 2009, which claims the priority of U.S. Provisional Application No. 61/081,482, filed Jul. 17, 2008, the entire contents of which are incorporated by reference herein.

GOVERNMENT INTERESTS

The inventors received material related to the subject matter of this application from the U.S. government under an agreement pursuant to 15 U.S.C. § 3710a, accordingly the U.S. government may have certain rights in the subject matter.

FIELD

Various embodiments described herein relate to live attenuated viral vaccines and systems and methods for making and administering such vaccines.

BACKGROUND

In the discussion that follows, reference is made to certain structures and/or methods. However, the following references should not be construed as an admission that these structures and/or methods constitute prior art. Applicants expressly reserve the right to demonstrate that such structures and/or methods do not qualify as prior art.

Many RNA viruses, including Yellow Fever (YE) virus and Venezuelan Equine Encephalitis (VEE) virus, are dangerous human pathogens. VEE is a Category B and YF is a Category C Priority Pathogen as categorized by NIE/NIAID.

The VEE virus is a positive single-stranded RNA arbovirus that belongs to the Alphavirus genus of the Togaviridae family. The virus is transmitted primarily by mosquitoes, which bite an infected animal and then bite and feed on another animal or human. VEE currently is rare in the U.S. A major epizootic in horses occurred in Texas, but only about 100 laboratory-confirmed cases in humans have been documented. However, changing climate may favor establishment of the virus in warmer areas of the U.S. Additionally, VEE is a potential biological weapon and bioterrorism agent.

The YF virus is also a positive single-stranded RNA arbovirus. However, unlike VEE, the YE virus belongs to the family Flaviviridae. YF disease occurs mostly in Africa and South America. Human infection begins after deposition of viral particles through the skin by an infected mosquito. The disease is frequently severe. More moderate cases can occur as a result of previous infection by another flavivirus. There is a difference between disease outbreaks in rural or forest areas and in urban areas (Barnett, 2007). Disease outbreaks in towns and non-native people can be more serious because of higher densities of mosquito vectors and higher population densities. As of 2001, the World Health Organization (WHO) estimates that YF virus causes 200,000 illnesses and 30,000 deaths every year in unvaccinated populations. In most cases, supportive therapy is required for YF patients. Fluid replacement, transfusion of blood derivatives, and other measures are used in severe cases.

Live attenuated viruses have been developed to serve as vaccines for many RNA viruses such as VEE and YF, poliomyelitis, influenza, measles, mumps, rabies, and rubella viruses. Traditional live attenuated RNA virus vaccines comprise live attenuated RNA viruses that are injected into the vaccine recipient. The injected virus delivers its RNA genome into the cells, which results in production of viral antigens as well as progeny attenuated viruses in the tissues of the vaccine recipient. This leads to the elicitation of an immune response that protects against the counterpart non-attenuated virus.

SUMMARY

This application provides vectors comprising DNA encoding an infectious RNA molecule and an RNA polymerase promoter, where the DNA encoding an infectious RNA molecule is operably linked to the RNA polymerase promoter and the infectious RNA molecule encodes a Yellow Fever (YF) virus. In certain embodiments, the YF virus is non-pathogenic. Also described are vaccines for Yellow Fever (YE) comprising the vectors described above, and methods for using the vaccines to immunize against a YE virus. Also described are homogeneous clonally purified live attenuated virus prepared from cultured cells transfected with the vector, vaccines for YE comprising the same, and methods for using the vaccines to immunize against a YE virus.

This application also provides vectors comprising DNA encoding an infectious RNA molecule and an RNA polymerase promoter, where the DNA encoding an infectious RNA molecule is operably linked to the RNA polymerase promoter and the infectious RNA molecule encodes a Venezuelan Equine Encephalitis (VEE) virus. In certain embodiments, the VEE virus is non-pathogenic. Also described are vaccines for Venezuelan Equine Encephalitis (VEE) comprising the vectors described above, and methods for using the vaccines to immunize against a VEE virus. Also described are homogeneous clonally purified live attenuated virus prepared from cultured cells transfected with the vector, vaccines for VEE comprising the same, and methods for using the vaccines to immunize against a VEE virus.

This application also provides vectors comprising a DNA encoding an infectious RNA molecule and a cytomegalovirus (CMV) RNA polymerase promoter, where the DNA encoding an infectious RNA molecule is operably linked to the CMV RNA polymerase promoter, the CMV RNA polymerase promoter is located from about 12 to about 18 nucleic acid residues upstream of the 5′ end of said DNA encoding an infectious RNA molecule, and the infectious RNA molecule encodes an attenuated RNA virus. In certain embodiments, the attenuated RNA virus is an alphavirus or a flavivirus.

This application also provides methods for attenuating an RNA virus, comprising inserting two RNA dependent RNA promoters into the cDNA encoding the RNA virus, whereby the nucleocapsid and glycoproteins are separately expressed from independent promoters.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Schematic representation of iDNA based VEE TC-83 vaccines. (A) Full-length cDNA corresponding to the TC-83 RNA genome is cloned into the DNA containing functional DNA-dependent RNA polymerase promoter, for example CMV promoter. Location of CMV promoter, 26S promoter, poly-A, transcription termination, and ribozyme (optional) sequences are shown. (E) Example of the modified, iDNA-based TC-83 vaccine, in which TC-83 capsid and glycoprotein genes are expressed from independent promoters. Location of the promoters is shown. The transcription start site can be modified by varying the distance between the 3′ end of the CMV promoter and the 5′ end of the TC-83 coding sequence.

FIG. 2. Administration of the TC-83 iDNA vaccine into cells in vitro or in vivo. Injection of the TC-83 iDNA vaccine under control of DNA-dependent RNA polymerase promoter (see FIG. 1) into cells in vitro or in vivo is shown. As a result of TC-83 iDNA vaccine administration, the TC-83 live attenuated virus vaccine is generated. If administered in vivo, production of TC-83 vaccine in the tissues of the patient elicits immune response to the TC-83 vaccine.

FIG. 3. Schematic representation of iDNA-based YF17D vaccine. Full-length cDNA corresponding to the 17D RNA genome is cloned into the DNA containing functional RNA polymerase promoter, for example CMV promoter. Location of CMV promoter, polyA, transcription termination, and ribozyme sequences are shown.

FIG. 4. Administration of the recombinant YF17D iDNA vaccine into cells in vitro or in vivo. Injection of the 17D iDNA vaccine containing YF17D cDNA under control of DNA-dependent RNA polymerase promoter into cells in vitro or in vivo is shown. As a result of 17D iDNA vaccine administration, the 17D live attenuated virus vaccine is generated. If administered in vivo to the tissues of vaccine recipient, production of YF17D vaccine in the tissues of the patient leads to elicitation of immune response to the 17D vaccine.

FIG. 5. Immunofluorescence assay (IFA) of CHO cells transfected with (A) VEE TC-83 iDNA vaccine, Clone 13-2 (FIG. 6); and (B) p3-10 DNA expressing TC-83 structural proteins (control). Focus of TC-83-positive cells is visible on panel (A), whereas panel (B) shows individual TC-83-positive cells. Cells are transfected with DNA vaccine using Eugene 6 transfection reagent or a similar gene transfer method. Transfected cells are incubated at 37° C. in 5% CO₂ incubator. Following 24 hr incubation, cells are fixed with cold acetone, and IFA is done using rabbit antibody specific for TC-83 antigen. Then, cells are incubated using rhodamine-conjugated antibody for rabbit IgG and observed using fluorescent microscopy.

FIG. 6. iDNA sequence fragment from pAA_TC83 plasmid (Clones #13-1; 13-2) containing the TC-83 cDNA downstream from CMV promoter (SEQ ID NO: 1). Locations of CMV promoter, 26 S promoter, and polyA site are indicated.

FIG. 7. iDNA sequence fragment of modified pAA_TC-83_C_GP plasmid (Clone #12) containing two TC-83 26S promoters (SEQ ID NO: 2). Locations of CMV promoter, 26S promoters, and polyA site are indicated.

FIG. 8. iDNA sequence fragment of pCMV_YF17D containing the YF17D cDNA downstream from CMV promoter and hepatitis a ribozyme and BCH transcription termination and polyadenylation cassettes downstream from 3′end of the YF17D sequence (SEQ ID NO: 3).

FIG. 9. Optimization of the distance between the 3′ end of the CMV promoter and the 5′ end of the TC-83 cDNA by encapsidation assay using HA- or N-vectors and DNA c-helpers.

FIG. 10. Transfection of CHO cells with TC-83 iDNA #13-1 (wild-type) results in rapid expression of TC-83 antigen in CHO cells.

FIG. 11. Transfection of CHO cells with TC-83 iDNA #12 (double 26S promoter) results in delayed expression of TC-83 antigen in CHO cells.

FIG. 12. TC-83 viruses generated from infectious clones in vitro are avirulent in BALE/c mice. Cloned TC-83 viruses are generated by transfection of CHO cells using electroporation with infectious TC-83 vaccine cDNA clones #12 and #13-1. Viruses are inoculated in mice according to standard USAMRIID protocol (Dr. Michael Parker, USAIVIRI1D, Ft, Detrick, Md.).

FIG. 13. Synthetic oligonucleotides of varying lengths (SEQ ID NOS: 4-14, from top to bottom) for creating a series of “capsid iDNA” plasm ids in which the distance between the promoter and the iDNA varies from 8 to 25 base pairs (see Example 8). The capitalized and bolded A shows the 5′ end of the VEE sequence (in TC-38, the start codon is ATA rather than ATO; see the ATA nucleotides at positions 704-706 in SEQ ID NO: 1).

DETAILED DESCRIPTION

Described herein are compositions for eliciting an immune response or a protective immunity against Yellow Fever (YF) or Venezuelan Equine Encephalitis (VEE) viruses. In one embodiment, the compositions comprise vaccines for preventing and/or treating YF or VEE virus associated diseases. Also described are methods of making, using and testing the same.

Live attenuated, cell-culture derived TC-83 vaccine for VEE has been developed previously. TC-83 contains attenuating mutations (Kinney et al., 1993). The current TC-83 vaccine is fully licensed for veterinary use in horses and was used successfully during 1970-1971 Texas epizootic. The vaccine has also been approved for use in people as an Investigational New Drug (IND). The TC-83 vaccine provides protection against many epizootic strains. The TC-83 vaccine has been used as part of safety programs and was important in protecting individuals working with infected animals and virus preparations. To date, the vaccine has been administered to-9,000 people. Another human IND vaccine, C-84, has been prepared from formalin-inactivated TC-83 vaccine. Because of the history of successful use as a vaccine in people, the TC-83 vaccine is also a promising vaccine vector, which can be used as a carrier of therapeutic or vaccine-relevant genes (Pushko P., U.S. Patent Application No. 2006/0198854, Vector platforms derived from the alphavirus vaccines).

Because there is no specific therapy for YF, vaccination is the only effective medical countermeasure. Current YF vaccine is a live, attenuated virus preparation made from the 17D YF virus strain (Smithburn et al., 1956). The 17D live virus vaccines have been considered to be safe and effective (Monath, 2001). The 17D YF vaccine virus is the foundation for both the 17D-204 and 17DD lineages. Vaccine 17D-204 is used in the U.S. and Australia, whereas vaccine 17DD is used in Brazil. Sequencing has revealed that the 17D-204 and 17DD vaccine types are not identical, which reflects accumulation of genetic mutations during multiple passages of virus seeds. With safety record in humans, the YF17D is also a promising vector for the development of vaccines against flavivirus-related pathogens (e.g. chimeric YF17D-based vaccines against Japanese encephalitis, dengue, and West Nile virus (Pugachev et al, 2005) as well as against pathogens outside the flavivirus genus such as malaria (Tao et al., 2005) and Lassa virus (Bredenbeek et al., 2006).

Described herein are iDNA molecules expressing the RNA genome of live attenuated viruses and methods for using the same. In certain embodiments, when iDNA is injected into the cultured cells in vitro, RNA of live attenuated virus is generated in the cells by in vivo transcription. This initiates production of progeny attenuated viruses in the medium from cultured cells. Such homogenous, clonally pure live attenuated virus can be used for vaccination as improved, homogeneous live attenuated vaccine. In other embodiments, when iDNA is injected into the cells of a vaccine recipient, RNA of live attenuated virus is generated by in vivo transcription in the tissues. This initiates production of progeny attenuated viruses in the tissues of vaccine recipient, as well as elicitation of effective immune response to live attenuated virus. Similarly to any DNA, the iDNA can be made in bacterial cells and represents a stable molecule.

In certain embodiments, the iDNA molecules are vectors comprising DNA encoding an infectious RNA molecule, where the infectious RNA molecule in turn encodes a YF or a VEE virus. The DNA encoding an infectious RNA molecule can be operably linked to an RNA polymerase promoter, and is generally modified to encode a non-pathogenic (attenuated) YF or VEE virus.

In certain embodiments, the iDNA (infectious DNA) molecules comprise the VEE TC-83 or the YF YF17D cDNA. For example, an exemplary iDNA-based VEE vaccine comprises a DNA molecule that contains the complete cDNA copy of the RNA genome of the TC-83 live attenuated virus. In this iDNA molecule, the TC-83 cDNA is placed downstream from an RNA polymerase promoter, such as the CMV promoter. When such an iDNA molecule is introduced into cells in vitro, the TC-83 viral RNA is generated in the cells. The resulting TC-83 RNA is “infectious” and initiates production of the TC-83 live attenuated virus vaccine in the cells. Such TC-83 virus vaccine can be harvested from cultured cells and used for vaccination according to current practices. In certain embodiments, the vaccine that is generated from the TC-83 iDNA represents homogeneous progeny virus generated from the same, well-characterized, stable DNA. Because the same, clonally purified, iDNA is used for the introduction of the vaccine lots, such vaccine will in certain embodiments have greater uniformity and lot-to-lot consistency compared to current vaccines, which can accumulate mutations during virus passages.

Alternatively, iDNA vaccine containing the TC-83 cDNA can be administered to the vaccine recipient directly. Such iDNA administration to the vaccine recipient initiates production of the TC-83 virus vaccine in the tissues of the patient in vivo, which provides successful vaccination against VEE.

Similarly, iDNA-based YF vaccines can comprise a DNA molecule that contains the cDNA copy of the RNA genome of the YF17D live attenuated virus. In this iDNA molecule, the YF17D cDNA copy can be placed downstream from an RNA polymerase promoter, for example the cytomegalovirus (CMV) promoter. When such iDNA molecule is introduced into cells in vitro or administered directly to the tissues of vaccine recipient in vivo, the 17D viral RNA is generated by transcription from the RNA polymerase promoter. The resulting YF17D RNA is infectious and initiates production of the YF17D live attenuated vaccine. When injected into tissues of a vaccine recipient in vivo, such YF17D-based iDNA provides successful vaccination of the patient against YF.

The TC-83 or YF17D cDNA can be modified to ensure sufficient attenuation and/or to introduce other characteristics, while still maintaining infectivity and the desired therapeutic effect. In certain embodiments, the cDNA is modified by insertion, deletion, and/or substitution of one or more of the nucleotides in the TC-83 or YF17D cDNA sequence. For example, the modified cDNA can have at least 50%, 60%, 70%, 80%, or 90% sequence identity with the TC-83 or YF17D sequence, such as at least 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity.

Examples of modified cDNAs include a DNA having an additional 26S promoter in the modified TC-83 iDNA Clone 12 (see example 3, Table I). This modification slows the development of TC-83-positive foci, which is a sign of additional attenuation caused by insertion of the additional 26S promoter in this construct (FIG. 1, B). Such additional attenuation can improve the TC-83 vaccine and reduce adverse effects associated with this vaccine. In this example, an additional 26S promoter could be inserted so that the TC-83 nucleocapsid and glycoproteins are generated from independent promoters (FIG. 1B). Thus, the TC-83 26S promoter is duplicated, and the capsid and glycoproteins are generated from the two 26S promoters. Other modification can be made to increase the stability of the iDNA in E.coli or in target cells, or to increase stability of iDNA in E.coli cells.

Additionally, other genes or gene fragments, including genetic material from other alphaviruses, or from unrelated sources such other viruses, bacteria, microorganisms, other organisms, plants, animals, or/and humans could be inserted into the iDNA. In such cases, the modified TC-83 or YF17D iDNA could serve as a vector for expression of heterologous genes in vitro or in vivo.

Described herein are specialized vectors for preparation of iDNA vaccines. However, it will be appreciated by those skilled in the art that the iDNA described herein can be formed using any suitable vector. In general, a vector is a nucleic acid molecule (typically DNA or RNA) that serves to transfer a passenger nucleic acid sequence (i.e., DNA or RNA) into a host cell. Three common types of vectors include plasmids, phages and viruses. In an exemplary embodiment, the vector is a plasmid. The present iDNA vaccines can he comprised of DNA that is produced as a plasmid that can be introduced into animal tissue and therein is expressed by animal cells to produce a messenger ribonucleic acid (mRNA) molecule approximately the size of the YF or the VEE genome, which is translated to produce viral polyproteins. The viral polyproteins in turn are processed by cellular machinery to provide a full set of YF or VEE proteins that are capable of initiating replication of the above primary RNA transcript and thus initiating the virus replication cycle in animal tissue into which the above DNA plasmid was introduced.

Suitable and exemplary plasmid vectors that have been used in conventional DNA vaccines include, but are not limited to pBR322 (ATCC #31344); pUC19 (ATCC #37254); pcDNA3.1 (Invitrogen, Carlsbad Calif, 92008; Cat. NO. V385-20); pNGVL (National Gene Vector Laboratory, University of Michigan, Mich.); p414cyc (ATCC#87380), p414GALS (ATCC #87344), pBAD18 (ATCC #87393), pBLCAT5 (ATCC #77412), pBluescriptlIKS, (ATCC #87047), p135LI30 (ATCC #87145), pCM182 (ATCC #87656), pCMVtkLUC (ATCC #87633), pECV25 (ATCC#77187), pGEM-7zf (ATCC #87048), pGEX-KN (ATCC #77332), pJC20 (ATCC #87113, pUB110 (ATCC #37015), pUB18 (ATCC #37253).

The iDNA described herein is also under the control of a suitable promoter. For eukaryotic expression, examples of suitable promoters include the cytomegalovirus (“CMV”) early promoter, the Rous sarcoma virus (“RSV”) LTR promoter, and the SV40 promoter.

The following describes exemplary methods for making iDNA vectors and vaccines:

The cDNA fragment corresponding to the full-length TC-83 RNA is derived by reverse transcription and polymerase chain reaction (RT-PCR) by using the TC-83 viral RNA and the TC-83 sequence-specific oligonucleotide primers. TC-83 viral RNA is extracted from the TC-83 vaccine using phenol extraction or other methods. The TC-83-specific oligonucleotide primers can contain additional functional elements, including, but not limited to, restriction enzyme sites, transcription terminators, polyadenylation signals, ribozymes, etc.

Alternatively, two or more cDNA fragments encompassing the entire TC-83 RNA are generated using RT-PCR. Then, such cDNA fragments are assembled within a single plasmid so that they comprise the full-length cDNA corresponding to the full-length TC-83 RNA, as described in the previous paragraph.

Alternatively, the TC-83 cDNA, as described in the previous paragraphs, is generated by using chemical synthesis or a combination of chemical synthesis or/and PCR or/and RT-PCR.

The cDNA fragment corresponding to the full-length RNA is cloned into the DNA containing a functional RNA polymerase promoter, for example CMV promoter (FIG. 1A). An example of such resulting recombinant iDNA sequence is shown (FIG. 6). As a result of transcription in vitro or in vivo of such iDNA, functional infectious TC-83 RNA containing one or more attenuating mutations is generated. The distance between the promoter and the TC-83 cDNA can be optimized to ensure the desired level of RNA expression. In certain embodiments, the distance between the GAGCTC 3′-end of the CMV promoter (indicated at nucleotide (nt) 687 with an arrow in FIG. 6), and the 5′-end of the TC-83 cDNA (indicated at nucleotide 703 with another arrow in FIG. 6), is 15(±3) base pairs (bp). This allows efficient transcription and production of TC-83 RNA. For comparison, according to Invitrogen, the CMV transcription start site would be located at nt 697, which is 9 at from the GAGCTC 3′ end of the CMV promoter within the pcDNA3.1(−) plasmid. Similarly, the 3′ end of the TC-83 cDNA can be followed by ribozymes, transcription termination sequences, poly-A, as well as other nucleotides arid signals to ensure optimal production of functionally active RNA. In a preferred embodiment, the distance between the 3′ end of TC-82 cDNA (at 12170, FIG. 6) and the poly-A site is 184 bp and can vary from between 0 to about 500 bp.

Alternatively, the TC-83 nucleocapsid and glycoproteins are expressed from independent promoters (FIG. 1B).

The resulting recombinant plasmid iDNA containing the TC-83 cDNA under control of the RNA polymerase promoter (FIG. 1A,B) is generated and purified from E. coli cells. Purified iDNA is then introduced into cultured eukaryotic cells, for example into Chinese hamster ovary (CHO) cells, baby hamster kidney (BHK-21), or other susceptible cells (FIG. 2). DNA is administered to cells by injection, gene gun, electroporation, liposome transfection, or other gene transfer method. In the cells, the full-length infectious TC-83 RNA is generated by transcription, which initiates the production of TC-83 live attenuated virus in cultured cells and release of TC-83 virus in the medium (FIG. 2). The TC-83 virus is harvested from the cell cultures, formulated, and used as a VEE vaccine according to the current practice.

Alternatively, the recombinant iDNA containing the TC-83 cDNA (FIG. 1) is introduced into the vaccine recipient directly in vivo. The iDNA is administered into vaccine recipient tissues by injection, electroporation, liposome transfection, gene gun, or other genetic transfer method. In the tissues of vaccine recipient, the full-length infectious TC-83 RNA is generated by transcription, which initiates production of TC-83 live attenuated virus in vivo. The TC-83 virus antigens are released from the cells in vivo in the tissues, which initiates induction of effective immune response to TC-83 vaccine.

Similar to the TC-83 iDNA described above, a YF17D iDNA includes the YF17D cDNA. Full-length YF17D cDNA is derived from the full-length viral RNA or assembled from two or more fragments or synthesized by chemical means as described above for the TC-83. The full-length YF17D cDNA is placed under the control of a functional RNA polymerase promoter, as shown in FIG. 4A. In certain embodiments, the distance between the GAGCTC 3′-end of the CMV promoter and the 5′-end of the TC 83 cDNA, is 15(±3) bp as described above for TC-83. This allows for efficient transcription and production of YF17D RNA. Ribozyme, transcription termination and poly (A) cassettes are placed as required downstream from the 3′ end of the YF17D cDNA to ensure correct transcription and polyadenylation of functional YF17D RNA transcripts. As a result of YF17D iDNA transcription in vitro or in vivo, functional infectious YF17D RNA (optionally containing one or more additional attenuating mutations) is generated. As seen in FIG. 4, transfection of BHK-21 cells with a full-length YF17D iDNA containing YF17D cDNA under control of the CMV promoter results in transcription of infectious RNA, translation, correct post-translational processing of polyprotein, assembly and release of infectious YF17D particles.

As noted above, modifications can be made to the full-length YF17D as well TC-83 cDNA constructs. Optimization of attenuation may additionally improve the YF17D iDNA vaccine and reduce adverse effects including viscerotropic disease associated with YF17D vaccination (Monath, 2007).

In certain embodiments, the methods described herein comprise administering a composition or a DNA vaccine comprising iDNA encoding for an attenuated YF cr VEE virus in an acceptable pharmaceutical carrier to a subject in need thereof.

The amount of iDNA present in the compositions or in the DNA vaccines described herein is preferably a therapeutically or pharmaceutically effective amount. A “therapeutically effective amount” of iDNA is that amount necessary so that the nucleotide sequence coding for the YF or VEE polypeptide performs its immunological role without causing overly negative effects in the host to which the composition is administered. The exact amount of plasmid to be used and the composition/vaccine to be administered will vary according to factors such as the strength of the transcriptional and translational promoters used, the type of condition being treated, the mode of administration, as well as the other ingredients in the composition. In one embodiment, the composition or the vaccine formulation comprises from about 1 ng to about 1 mg of plasmid

The immunogenicity of the DNA vaccines and pharmaceutical compositions can be modified by formulating with one or more pharmaceutically acceptable adjuvants or immunostimulants, such as alpha-interferon, beta-interferon, gamma-interferon, granulocyte macrophage colony stimulator factor (“GM-CSF”), macrophage colony stimulator factor (“M-CSF”), interleukin 2 (“IL-2”), interleukin 12 (“11,12”), and CpG oligonucleotides. For preparing such compositions, methods well known in the art can be used. In certain embodiments, the iDNA is generated in E.coli cells as a plasmid DNA, containing unmethylated CpG motifs and itself constitutes an immunostimulating molecule that activates the immune system via toll-like receptors.

Subcutaneous injection, intradermal introduction, impression through the skin, and other modes of administration such as intraperitoneal, intravenous, oral, or inhalation delivery are also suitable. For example, vectors containing the iDNA can be introduced into the desired host by methods known in the art, for example, transfection, electroporation, microinjection, microparticles, microcapsules, transduction, cell fusion, DEAE dextran, calcium phosphate precipitation, lipofection (lyposome fusion), use of a gene gun (particle bombardment), or a DNA vector transporter (see, e.g., Wu et al., 1992, J. Biol. Chem. 267:963.967; Wu and Wu, 1988, J. Biol. Chem. 263:14621-1 4624).

As used herein, the term “treating,” “treatment” and the like are used herein to generally mean obtaining a desired pharmacological and/or physiological effect, and refer to a process by which the symptoms of a YF or VEE associated disease are completely eliminated or ameliorated to any clinically and/or quantitatively measurable degree. The term “preventing” refers to a process by which a YF or VEE associated disease is obstructed and/or delayed. The compositions and vaccines described herein comprise iDNA (iDNA) capable of producing a live attenuated virus, In one embodiment, the live attenuated virus is produced in vivo.

As used herein, the term “immune response” includes a T cell response, increased serum levels of antibodies to an antigen, the presence of neutralizing antibodies to an antigen (such as a YE or VEE polypeptide), or combinations thereof. The term “protection” or “protective immunity” includes the ability of the serum antibodies or T cell response induced during immunization to protect (partially or totally) against disease or death caused by YF or VEE viruses,

The “subject” is a vertebrate, such as a mammal. Mammals include, but are not limited to, humans, other primates, rodents, farm animals, sport animals (horses, etc.) and pets. In certain embodiments, the subject is a human. In other embodiments, the methods find use in experimental animals (such as all species of monkeys), in veterinary application and/or in the development of animal models for disease. In certain embodiments, the vaccine is a VEE (such as TC-83) vaccine and the subject is a horse. A “subject in need thereof” refers to any subject, patient, or individual who could benefit from the methods described herein.

The term “therapeutically (or “pharmaceutically”) effective dose” or “therapeutically (or “pharmaceutically”) effective amount” means a dose or amount that produces the desired effect for which it is administered. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques.

The term “pharmaceutically acceptable” means approved by a regulatory agency of the federal or a state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly, in humans.

The term “carrier” refers to a diluent, adjuvant, excipient, or vehicle with which the iDNA is administered. Such pharmaceutical carriers can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, combinations thereof and the like. Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol, combinations thereof and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. These compositions can take the form of solutions, suspensions, emulsion, tablets, pills, capsules, powders, sustained-release formulations, combinations thereof and the like, The composition can be formulated as a suppository, with traditional binders and carriers such as triglycerides. Oral formulations can include standard carriers such as pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, cellulose, magnesium carbonate, combinations thereof; etc. Examples of suitable pharmaceutical carriers are described in “Remington's Pharmaceutical Sciences” by E. W. Martin.

Thus, as used herein, the term “pharmaceutically acceptable carrier” means, but is not limited to, a vehicle for containing the iDNA that can be injected into a mammalian host without adverse effects. Suitable pharmaceutically acceptable carriers known in the art include, but are not limited to, gold particles, sterile water, saline, glucose, dextrose, or buffered solutions, combinations thereof and the like. Carriers may include auxiliary agents including, but not limited to, diluents, stabilizers (i.e., sugars and amino acids), preservatives, wetting agents, emulsifying agents, pH buffering agents, viscosity enhancing additives, colors, combinations thereof and the like.

As used herein, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “vaccine” includes a plurality of such vaccines and reference to “the dosage” includes reference to one or more dosages and equivalents thereof known to those skilled in the art, and so forth.

The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosure. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed. All publications, patents, patent applications and other references cited herein are hereby incorporated by reference.

While the disclosure has been described in detail with reference to certain embodiments thereof; it will be apparent to one skilled in the art that various changes can be made, and equivalents employed, without deviating from the scope of the disclosure, In addition, the following examples are illustrative of the methods described herein and should not be considered as limiting the foregoing disclosure in any way.

EXAMPLES Example 1

Preparation of TC-83 iDNA. Total RNA is extracted from the TC-83 vaccine using phenol extraction. The cDNA corresponding to the full-length TC-83 RNA is derived by reverse transcription and polymerase chain reaction (RT-PCR) using extracted TC-83 viral RNA and the TC-83 sequence-specific oligonucleotide primers.

The cDNA fragment corresponding to the full-length TC-83 RNA is cloned into the plasmid vector pASP5 containing a functional CMV promoter (FIG. 1A, FIG. 6), which yields the TC-83 iDNA, clone 13-1 and clone 13-2. The distance between the 3′ end of the CMV promoter to 5′ end of the TC-83 cDNA is 15 bp as shown in FIG. 6. After transcription of such TC-83 iDNA in vitro or in vivo by cellular transcription machinery, functional infectious TC-83 RNA and TC-83 virus are generated.

The TC-83 iDNA can be easily modified to optimize functional characteristics, for example, the level of attenuation. For example, modified TC-83 cDNA, clone 12, is generated by duplicating the 26S promoter and placing the second 26S promoter upstream from the TC-83 glycoprotein genes (FIG. 1B, FIG. 7). In such a construct, the RNA that is generated from the CMV promoter expresses the TC-83 capsid and glycoproteins from independent 26S promoters. In order to ensure expression of the TC-83 proteins from such modified TC-831A, appropriate changes are made, for example, ATG codon is introduced at the 5′ terminus of the glycoprotein genes. The full-length RNA encoding cDNA of modified TC 83 (Clone 12) is introduced into the claimed plasmid vector pASP5 containing functional CMV promoter (FIG. 1B, FIG. 7). The distance between the 3′ end of CMV promoter to the 5′ end of modified TC-83 cDNA is 15 bp as shown in FIG. 7.

Example 2

Preparation of YF17D iDNA Total RNA is extracted from the YF17D vaccine using phenol extraction or a similar method. The cDNAs corresponding to the full-length 17D RNA is derived by reverse transcription and polymerase chain reaction (RT-PCR) using extracted 17D viral RNA and the 17D sequence-specific oligonucleotide primers. Alternatively, the full-length YF17D cDNA is assembled from two or more plasmids.

The cDNA fragment corresponding to the full-length RNA is transferred into the claimed plasmid vector pASP5 containing functional CMV promoter (FIG. 3), which results in YF17D iDNA (FIG. 8). The distance between the 3′ end of CMV promoter to the 5′end of YF17D cDNA is 15 bp as shown in FIG. 8 and described above for the TC-83 constructs. After transcription of YF17D iDNA in cells in vitro or in vivo, functional infectious YF17D RNA and YF17D virus are generated.

Example 3

Transfection of CHO cells with TC-83 iDNA vaccine. Plasmid DNA containing TC-83 iDNA is transfected into CHO cells using Fugene 6 transfection reagent (Roche Applied Sciences). Briefly, CHO cells are grown in 75 cm2 flasks, then rinsed with phosphate buffered saline (PBS) and trypsinized. Aliquot of CHO cell suspension is transferred into 6-well cell culture plates. Then, mixture of plasmid DNA and Fugene 6 reagent is added according to manufacturer's instructions. As plasmid DNA, the following constructs are used:

(1) VEE TC-83 modified iDNA, Clone 12 (FIG. 1B, FIG. 7);

(2) VEE TC-83 iDNA, Clone 13-1 (FIG. 1A, FIG. 6);

(3) VEE TC-83 iDNA, Clone 13-2 (FIG. 1A, FIG. 6);

(4) As a control, p3-10 DNA expressing TC-83 structural proteins only, is used.

As an additional control, untransfected CHO cells (5) are used. The iDNAs (1) through (3) contain the complete TC-83 cDNA and are expected to generate live TC-83 virus. As described above, the Clone 12 iDNA (1) contains duplicated 26S promoter to express TC-83 capsid and glycoproteins from two independent 26S promoters (FIG. 1B). In contrast, DNA (4) contain only a fragment of TC-83 corresponding to the TC-83 structural genes only and is not expected to generate live TC-83 virus.

An aliquot (0.3 ml) from transfected CHO cells from 6-well plates is seeded into 8-well chamber slides. Transfected CHO cells are incubated at 37° C. in 5% CO₂. Cell mortality is determined in 6-well plates daily by visual microscopy. Immunofluorescense assay (IFA) is performed at 24 hr post-transfection using 8-well chamber slides with antiserum that recognizes the TC-83 antigens, according to the method described in Pushko et al. (1997). The results are shown in Table I. Cells transfected with iDNAs (1) through (3) die within 5 days post-transfection, whereas CHO cells with control transfections (4) and (5) remain alive. Also, foci of cells expressing TC-83 antigens are detected by IFA at 24 hr post-transfection in the cells transfected with DNAs (2) and (3), thus indicating presence of live TC-83 virus (FIG. 5). The result indicates that introduction of iDNA-based TC-83 vaccines into cultured cells resulted in production of live TC 83 Bvirus.

TABLE I Transfection of CHO cells with the TC-83 vaccine iDNA CHO Cell Foci of Mortality after infected cells, iDNA Vaccine* DNA transfection** By IFA*** 1. VEE TC-83 modified iDNA, Yes None, only Clone 12 (FIG. 7) positive individual cells 2. VEE TC-83 iDNA, Clone Yes Yes 13-1 (FIG. 6) 3. VEE TC-83 iDNA, Clone Yes Yes 13-2 (FIG. 6) 4. p3-10 DNA expressing TC-83 No None, only structural proteins only positive (control) individual cells 5. Untransfected CHO cells No No (control) *DNA transfected into CHO cells is done in 6-well plates using Fugene 6 transfection reagent (Roche Applied Sciences) **Observed on day 5 after transfection. ***IFA, immunofluorescence assay, by using antiserum for TC-83 structural proteins.

Example 4

Transfection of BHK-12 cells with iDNA vaccine. Briefly, plasmid DNA containing YF17D iDNA is transfected into cultured cells (CHO, BHK-21, or similar cell lines) and assayed using standard methods as described in Example 3. The results are shown in Table II. Plaque assay is used to determine the titer of live YF17D virus generated in cells transfected with plasmid iDNA. These results indicate that introduction of iDNA-based 17D vaccine into cultured cells results in synthesis of virus-specific RNA and in production of live YF17D virus (Table II).

TABLE II Transfection of BHK-21 cells with plasmid DNA containing YF17D iDNA BHK Cell Mortality after YF17D titer, DNA transfection by plaque iDNA Vaccine* in vitro** assay*** 1. YF17D iDNA Yes 10⁸ pfu/ml 6. Untransfected BHK-21 cells No Not detected (control) *DNA transfected into BHK cells is done in 6-well plates using Fugene 6 transfection reagent (Roche Applied Sciences) **Observed on day 5 after transfection ***Assay performed on media collected from transfected cells 5 days post transfection.

Example 5 Infection of CHO Cells with TC-83 Virus Derived from iDNA-Transfected Cells

In order to confirm that live TC-83 virus is generated in the cells transfected with plasmid DNA containing the complete TC-83 cDNA, the medium is harvested from transfected cells (see example 3) and used to infect fresh CHO cells. Fresh CHO cells are infected in 8-well chamber slides with 100-fold diluted media harvested from transfected cells, and expression of TC-83 antigens is detected by IFA at 24 hr postinfection (Table III). The results indicate that media from cells transfected with iDNA-based TC-83 vaccines contain live, infectious TC-83 virus.

TABLE III Infection of fresh CHO cells with medium collected from CHO cells transfected with iDNA containing the full-length cDNA of TC-83 vaccine downstream from the CMV promoter* % cells positive for TC-83 DNA Vaccine Transfected Antigen, by IFA 1. VEE TC-83 modified iDNA, Clone 12 100 2. VEE TC-83 iDNA, Clone 13-1 80 3. VEE TC-83 iDNA, Clone 13-2 100 4. p3-10 DNA expressing TC-83 structural 0 proteins only (control) 5. Untransfected CHO cells (control) 0 *Medium collected from transfected cells 5 days posttransfection (Table I) is diluted 100-fold, then 100 mcL are used to infect fresh CHO cells in 8-well chamber slides for 1 hr at 37° C., 5% CO₂. Then, 300 mcL of complete medium is added and incubation is continued for 24 hr. **IFA 24 hr postinfection, by using antiserum for TC-83 structural proteins.

Example 6 Vaccination of Mice with TC-83 iDNA Vaccine

Experimental mice (BALM, C57BL/16, Swiss Webster outbred, or other susceptible strain) are injected intramuscularly, subcutaneously, and intradermally with a dose of each TC-83 iDNA vaccine (Clones 12, 13-1, 13-2, as indicated in Table I) ranging from 1 ng to 1 mg. The TC-83 iDNA vaccines are isolated from E.coli as plasmid DNA by using Promega Endo-free DNA isolation method. In 30 days, animals receive a second identical dose of the TC-83 iDNA vaccine. Serum samples from anesthetized animals are taken from the retroorbital sinus on days 0, 30, and 60. Immune response is determined by standard immunological methods including determination of serum antibody to TC-83 antigens in the serum of vaccinated animals by ELISA. Serum antibody to TC-83 antigens is detected suggesting successful B23vaccination with TC-83 iDNA vaccine.

Example 7 Vaccination of Mice with YF17D iDNA Vaccine

Experimental mice (BALB/c, C57BL/6, Swiss Webster outbred, or other susceptible strain) are injected intramuscularly, subcutaneously, and intradermally with a dose of each 17D iDNA vaccine (see DNA sequence on FIG. 7) ranging from 1 ng to 1 mg. The 17D iDNA vaccine is isolated from E.coli as plasmid DNA by using Promege Endo-free DNA isolation method. In 30 days, animals receive a second identical dose of the 17D iDNA vaccine, Serum samples from anesthetized animals are taken from the retroorbital sinus on days 0, 30, and 60. Immune response is determined by standard immunological methods including determination of serum antibbdy to YF 17D antigens in the serum of vaccinated animals by ELBA. Serum antibody to YE antigens is detected suggesting successful vaccination with YF17D iDNA vaccine.

Example 8 Optimization of Distance Between the 3′ End of CMV Promoter and the 5′ End of CD A. by Encapsidation Assay Using HA- or N-Vectors and the DNA e-Helpers

For the successful function of the iDNA, it is important to achieve efficient transcription of the functional, full-length TC-83 RNA from the iDNA plasmid. Therefore, it is important to optimize transcription including the distance between the end of the promoter and the start of the cDNA, in order to maximize the efficacy of synthesis of functional RNA. We construct a “small iDNA” that encodes only the capsid gene of TC-83 virus including regulatory regions. All other TC-83 genes are deleted from such “capsid iDNA”, Then, we insert synthetic oligonucleotides of varying lengths (see FIG. 13) between the CMV promoter and the “capsid iDNA” using Sacl site at the 3′ terminus of the CMV promoter. Thus, a series of “capsid iDNA” plasmids is made in which the distance between the promoter and the iDNA varies from 8 to 25 base pairs. Each capsid iDNA construct is transfected by electroporation into CHO cells along with (1) GP-helper RNA and (2) HA-vector RNA. The GP-helper RNA encodes the TC-83 glycoproteins, whereas HA-vector RNA encodes the HA gene of influenza. In the cotransfected CHO cells, the TC-83 capsid and GP proteins encapsidates the HA-vector into single-cycle particles. By titration of such particles using immunofluorescence assay (IFA) and HA antiserum, the titer of the particles is detected. In this system, the level of expression of capsid from the “capsid iDNA” is a rate-limiting factor and affects the titer of the particles.

We find that the optimal distance between the 3′-terminus of the CMV promoter and the 5′ end of the TC-83 capsid cDNA is 15 base pairs between the Sad site (the end of CMV promoter) and the start of cDNA (FIG. 9). We find that this optimal distance provided expression of functional capsid antigen at a maximum level. However, other capsid iDNA constructs with distances of 12 to 18 bp also provide detectable level of expression and high titers of particles. The data are confirmed in several experiments using titration of HA-vector. We also confirm these optimization results when we use for quantitation the N-vector expressing nucleoprotein gene instead of HA gene.

Example 9 TC-83 Viruses Generated from Infectious Clones In Vitro are Avirulent in BALB/c Mice

TC-83 viruses are generated by transfection of CHO cells with infectious TC-83 vaccine cDNA (iDNA), clones #12 and #13-1. Expression of TC-83 antigens is shown by TA at 24 hr post transfection in cells transfected with either iDNA (#12 and #13-1). Viruses are harvested from CHO cell cultures at 96 hr post transfection, after and the cytopathic effect (CPE) is apparent. The titer of each virus is determined by standard plaque assay in Vero cell monolayers. The virus generated from iDNA #13-1 has the titer of 7×107 FFUlml, whereas the virus generated from iDNA #12 does not show the plaques, suggesting slower formation of plaques and possibly, higher level of attenuation. Then, 10⁵ plaque forming units (PFU) of #13-1 virus are inoculated in BALB/c mice intramuscularly according to standard protocol. Virus generated from DNA #12 is not used for inoculation of animals, because the plaque titer cannot be determined. As a control, the wild type VEE virus (Trinidad strain) is inoculated into animals.

In the control VEE group, 10 out of 10 animals dies following inoculation, demonstrating the virulent nature of the control virus (FIG. 12). In contrast, virus generated from iDNA (#13-1) is avirulent in mice, as mice show no signs of disease, This result confirms that iDNA contains attenuated mutations derived from the TC-83 vaccine and that these attenuating mutations do not revert to the wild-type virulent phenotype during virus production from iDNA.

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The invention claimed is:
 1. A homogeneous clonally pure live attenuated virus prepared from cultured cells transfected with a vector comprising DNA encoding: (a) an infectious RNA molecule that encodes a non-pathogenic alphavirus; and (b) two RNA dependent RNA polymerase promoters; wherein the two RNA dependent RNA polymerase promoters are operatively linked to one or more portions of a capsid and a glycoprotein of the infectious RNA molecule.
 2. A vaccine for an infectious RNA virus comprising a therapeutically effective amount of a homogeneous clonally pure live attenuated virus prepared from cultured cells transfected with a vector comprising DNA encoding: (a) an infectious RNA molecule that encodes a non-pathogenic alphavirus; and (b) two RNA dependent RNA polymerase promoters; wherein the two RNA dependent RNA polymerase promoters are operatively linked to one or more portions of a capsid and a glycoprotein of the infectious RNA molecule.
 3. The vaccine according to claim 2, wherein the vaccine is in a form selected from the group consisting of a solution, a suspension, an emulsion, a tablet, a pill, a capsule, a powder, a sustained-release formulation, and combinations thereof.
 4. The vaccine according to claim 2, wherein the vaccine further comprises a pharmaceutically acceptable carrier.
 5. The vaccine according to claim 4, wherein the carrier comprises a sterile liquid.
 6. The vaccine according to claim 5, wherein the sterile liquid comprises water, a petroleum, an animal oil, a vegetable oil, a peanut oil, a soybean oil, a mineral oil, or a sesame oil.
 7. A homogeneous clonally purified live attenuated virus comprising: an infectious RNA molecule, and two RNA dependent RNA polymerase promoters, the two RNA dependent RNA polymerase promoters being operatively linked to one or more portions of a capsid and a glycoprotein of the infectious RNA molecule, wherein the infectious RNA molecule encodes a non-pathogenic alphavirus.
 8. The virus of claim 7, wherein at least one of the RNA dependent RNA polymerase promoter is a 26S promoter.
 9. The virus of claim 7, wherein both of the RNA dependent RNA polymerase promoter are 26S promoters.
 10. The virus of any one of claims 7-9, wherein the non-pathogenic alphavirus is a non-pathogenic Venezuelan Equine Encephalitis (VEE) virus.
 11. The virus of claim 1, wherein the non-pathogenic alphavirus is a non-pathogenic VEE virus.
 12. A method of producing a vaccine for an infectious RNA virus comprising transfecting cultured cells with a DNA vector comprising: (a) an infectious RNA molecule that encodes a non-pathogenic alphavirus; and (b) a eukaryotic RNA polymerase promoter; wherein the DNA encoding an infectious RNA molecule is operably linked to the RNA polymerase promoter.
 13. A vaccine for an infectious RNA virus comprising a therapeutically effective amount of a DNA vector comprising DNA encoding: (a) an infectious RNA molecule that encodes an alphavirus; and (b) a eukaryotic RNA polymerase promoter; wherein the DNA encoding the infectious RNA molecule is operably linked to the RNA polymerase promoter.
 14. A method for immunizing a mammal against an alphavirus comprising the step of administering to the mammal a vaccine comprising a therapeutically effective amount of a vector comprising: (a) an infectious RNA molecule that encodes a non-pathogenic alphavirus; and (b) a eukaryotic RNA polymerase promoter; wherein the DNA encoding an infectious RNA molecule is operably linked to the RNA polymerase promoter.
 15. A vaccine for a VEE virus associated disease comprising the vaccine of claim 2, the DNA vector of claim 13, and/or the virus of claim 1 or
 7. 16. Method of preventing a VEE virus associated disease in a subject, the method comprising: administering a therapeutically effective amount of the vaccine claim 2, the DNA vector of claim 13, and/or the virus of claim 1 or 7 to the subject. 